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Merge pull request #666 from broadinstitute/pd_merge_selectvariants_test 

Removed redundant SelectVariantsIntegrationTest, merged its only test i...
This commit is contained in:
Eric Banks 2014-06-24 21:19:46 -04:00
parent 42cfa3b53b 06d619e9aa
commit 92028027c9
2 changed files with 13 additions and 46 deletions
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13
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java
View File

@ -356,4 +356,17 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
executeTest(name, spec);
}
@Test
public void testInvalidJexl() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants" +
" -R "+b37KGReference +
" -V "+privateTestDir+"ac0.vcf" +
" -select 'vc.getGenotype(\"FAKE_SAMPLE\").isHomRef()'" +
" -o %s",
1,
UserException.class);
executeTest("InvalidJexl", spec);
}
}

46
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java
View File

@ -1,46 +0,0 @@
/*
* Copyright (c) 2012 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.gatk.tools.walkers.variantutils;
import org.broadinstitute.gatk.engine.walkers.WalkerTest;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import org.testng.annotations.Test;
public class SelectVariantsIntegrationTest extends WalkerTest {
@Test
public void testInvalidJexl() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants" +
" -R "+b37KGReference +
" -V "+privateTestDir+"ac0.vcf" +
" -select 'vc.getGenotype(\"FAKE_SAMPLE\").isHomRef()'" +
" -o %s",
1,
UserException.class);
executeTest("InvalidJexl", spec);
}
}